Hi all,
Occasionally I've seen TravisCI tool tests fail with an exeception ValueError: No JSON object could be decoded, e.g.
https://travis-ci.org/peterjc/galaxy_blast/jobs/107255016
... galaxy.jobs INFO 2016-02-16 14:17:41,118 Collecting metrics for Job 139 galaxy.jobs DEBUG 2016-02-16 14:17:41,143 job 139 ended (finish() executed in (1049.363 ms)) galaxy.model.metadata DEBUG 2016-02-16 14:17:41,154 Cleaning up external metadata files ... ====================================================================== ERROR: NCBI BLAST+ blastn ( ncbi_blastn_wrapper ) > Test-2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py", line 291, in test_tool self.do_it( td ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py", line 40, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py", line 41, in stage_data_in_history upload_wait() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py", line 278, in wait while not self.__history_ready( history_id ): File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py", line 297, in __history_ready history_json = self._get( "histories/%s" % history_id ).json() File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/requests/models.py", line 805, in json return complexjson.loads(self.text, **kwargs) File "/opt/python/2.6.9/lib/python2.6/json/__init__.py", line 307, in loads return _default_decoder.decode(s) File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 319, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 338, in raw_decode raise ValueError("No JSON object could be decoded") ValueError: No JSON object could be decoded -------------------- >> begin captured stdout << --------------------- ...
On this run there was no sign of an SQLite locking issue. This JSON problem went away on a re-run, sadly instead the test-set failed further on with an SQLite locking problem, see:
https://github.com/galaxyproject/galaxy/issues/1158#issuecomment-168714547
Does this "No JSON object could be decoded" point at a file system issue (perhaps a race condition)? From searching the email archive this exception (although not necessarily from the same area of the code) seems to occur most often where Galaxy is being used with a cluster. But here this is all running on a single TravisCI VM with the local job runner.
I appreciate there probably isn't enough information here to solve this, but perhaps we need better logging here - are the JSON files simply empty for example?
Regards,
Peter